merged_profile_matrix_cluster: Merged profile matrix clustering

In lakhanp1/chipmine: Analyze ChIP-seq Data

Description

This function join the multiple profile matrix and performs the k-means clustering on the merged profile matrix

Usage

merged_profile_matrix_cluster(
  name,
  exptInfo,
  genes,
  clusterStorePath,
  matrixBins = c(200, 200, 100, 10),
  source = "deeptools",
  k,
  kmIter = 200,
  kmStarts = 200,
  ...
)

Arguments

name	name of the newly mearged profile matrix
exptInfo	experiment info as data frame with information like sampleID, type, path etc
genes	A vector of gene IDs which are to be plotted
clusterStorePath	Path for storing/accessing the cluster information file.
matrixBins	A numeric vector with four elements
source	Method by which profile matrix was generated. One of "deeptools", "miao" or "normalizedmatrix".
k	number of cluster centers
kmIter	iter.max argument of stats::kmeans() function. Default: 200
kmStarts	nstart argument of stats::kmeans() function. Default: 200
...	other arguments for stats::kmeans() function

Value

A list with two elements:

• profileKm: kmeans clustering object returned by function profile_matrix_kmeans()

• mat: a merged profile matrix as dataframe

Examples

NA

lakhanp1/chipmine documentation built on March 6, 2021, 9:06 a.m.